Thanks Tsjerk, That works great, and thanks for the vectors I can see where I went wrong calculating them myself.
Thanks again, -Trayder On Fri, May 23, 2014 at 6:16 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Trayder, > > You can check the code of insane ( > http://cgmartini.nl/cgmartini/index.php/insane), which sets up such a > rhombic dodecahedron when -pbc optimal is given. Essentially, the routine > boils down to: > > 1. Determining the diameter of the protein in the XY directions > 2. Set the first vector u=(diam+pbcdistance, 0, 0) > 3. Set the second vector v=(u/2, cos30*u, 0) > 4. Set the third vector to w=(u/2, cos30*u/3, Z), where > Z=(protZlength+pbcdistance) > > Changing the Z-dimension of the box (or the whole box) can be done manually > (or using awk), changing the numbers of the last line in the gro file, > which corresponds to (ux vy wz uy uz vx vz wx wy). Finally, note that the > box (any box) is written in its triclinic representation, which is easiest > to handle mathematically. > > Hope it helps, > > Tsjerk > > > > On Fri, May 23, 2014 at 4:42 AM, Trayder Thomas > <trayder.tho...@monash.edu>wrote: > > > Hi, > > > > I'm trying to figure out how to construct a rhombic dodecahedron for a > > membrane system. > > The manual (Section 3.2.1) states: > > > > "There are two different orientations of a rhombic dodecahedron that > > satisfy equations 3.1, 3.2 and 3.3. The program editconf produces the > > orientation which has a square intersection with the xy-plane. This > > orientation was chosen because the first two box vectors coincide with > the > > x and y-axis, which is easier to comprehend. The other orientation can be > > useful for simulations of membrane proteins. In this case the > cross-section > > with the xy-plane is a hexagon, which has an area which is 14% smaller > than > > the area of a square with the same image distance. The height of the box > > (cz) should be changed to obtain an optimal spacing." > > > > I can't figure out how to construct the system with a hexagon on the x-y > > plane, I presume I can rotate the box but I can only visualise the result > > as a triclinic cell. > > I also can't figure out how to adjust the height of the box, editconf > only > > accepts a single magnitude for dodecahedron vector lengths. > > > > Any help would be greatly appreciated. > > Thanks in advance, > > > > -Trayder > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
